Workflow to process tandem MS files and build MassBank records

[Up] [Top]

Documentation for package ‘RMassBank’ version 3.0.0

Help Pages

A C D E F G I L M N O P R S T U V misc

-- A --

add.formula Calculations on molecular formulas
addMB MassBank-record Addition
addPeaks Add additional peaks to spectra
addPeaksManually Addition of manual peaklists
addProperty Add and initialize dataframe column
addProperty-method Add and initialize dataframe column
aggregateSpectra Aggregate analyzed spectra
analyzeMsMs Analyze MSMS spectra
analyzeMsMs.formula Analyze MSMS spectra
analyzeMsMs.intensity Analyze MSMS spectra
annotator.default Generate peak annotation from peaklist
archiveResults Backup 'msmsWorkflow' results

-- C --

checkIsotopes Checks for isotopes in a 'msmsWorkspace'
checkSpectra Check if a spectra set is found, complete, empty
checkSpectra-method Check if a spectra set is found, complete, empty
cleanElnoise Remove electronic noise
cleanElnoise-method Select peaks from aggregate table
combineMultiplicities Combine workspaces for multiplicity filtering
createMolfile Create MOL file for a chemical structure
CTS.externalIdSubset Select a subset of external IDs from a CTS record.
CTS.externalIdTypes Find all available databases for a CTS record

-- D --

dbe Calculate Double Bond Equivalents
deprofile De-profile a high-resolution MS scan in profile mode.
deprofile.fwhm De-profile a high-resolution MS scan in profile mode.
deprofile.localMax De-profile a high-resolution MS scan in profile mode.
deprofile.scan De-profile a high-resolution MS scan in profile mode.
deprofile.spline De-profile a high-resolution MS scan in profile mode.

-- E --

exportMassbank Export internally stored MassBank data to files

-- F --

fillback Fill back reanalyzed / refiltered peak info into spectra
filterLowaccResults Filter peaks with low accuracy
filterMultiplicity filterMultiplicity
filterPeakSatellites Filter satellite peaks
filterPeaksMultiplicity Multiplicity filtering: Removes peaks which occur only once in a n-spectra set.
findCAS Find compound information
findEIC Extract EICs
findFormula Find compound information
findLevel Find compound information
findMass Calculate exact mass
findMsMsHR Extract MS/MS spectra for specified precursor
findMsMsHR.direct Discontinued: find MS/MS spectrum from open raw file
findMsMsHR.mass Extract MS/MS spectra for specified precursor
findMsMsHR.ticMS2 Extract an MS/MS spectrum from MS2 TIC
findMsMsHR.ticms2 Extract an MS/MS spectrum from MS2 TIC
findMsMsHRperxcms Read in mz-files using XCMS
findMsMsHRperxcms.direct Read in mz-files using XCMS
findMz Find compound information
findMz.formula Find the exact mass +/- a given margin for a given formula or its ions and adducts.
findName Find compound information
findProgress Determine processed steps
findRt Find compound information
findSmiles Find compound information
flatten Flatten, or re-read, MassBank header blocks
formulastring.to.list Interconvert molecular formula representations

-- G --

gatherCompound Compose data block of MassBank record
gatherData Retrieve annotation data
gatherDataBabel Retrieve annotation data
gatherDataUnknown Retrieve annotation data
gatherPubChem Retrieve supplemental annotation data from Pubchem
gatherSpectrum Compose data block of MassBank record
getAnalyticalInfo Compose data block of MassBank record
getCactus Retrieve information from Cactus
getCompTox Retrieves DTXSID (if it exists) from EPA Comptox Dashboard
getCSID Retrieve the Chemspider ID for a given compound
getCtsKey Convert a single ID to another using CTS.
getCtsRecord Retrieve information from CTS
getData Get data frame with all present peak data
getData-method Get data frame with all present peak data
getMolecule Create Rcdk molecule from SMILES
getPcId Search Pubchem CID

-- I --

is.valid.formula Check validity of formula

-- L --

list.to.formula Interconvert molecular formula representations
loadInfolist Load MassBank compound information lists
loadInfolists Load MassBank compound information lists
loadList Load compound list for RMassBank
loadMsmsWorkspace Create new empty workspace or load saved data for 'msmsWorkflow'
loadRmbSettings RMassBank settings
loadRmbSettingsFromEnv RMassBank settings

-- M --

makeMollist Write list.tsv file
makePeaksCache Generate peaks cache
makeRecalibration Recalibrate MS/MS spectra
mbWorkflow MassBank record creation workflow
mbWorkspace-class Workspace for 'mbWorkflow' data
mergePeaks.df Merge peaks for spectra merging, FT shoulder elimination etc.
msmsRead Extracts and processes spectra from a specified file list, according to loaded options and given parameters.
msmsRead.RAW Extracts and processes spectra from a list of xcms-Objects
msmsWorkflow RMassBank mass spectrometry pipeline
msmsWorkspace-class Workspace for 'msmsWorkflow' data
multiply.formula Calculations on molecular formulas

-- N --

newMbWorkspace Create new workspace for 'mbWorkflow'
newMsmsWorkspace Create new empty workspace or load saved data for 'msmsWorkflow'

-- O --

order.formula Order a chemical formula correctly

-- P --

parseMassBank MassBank-record Parser
parseMassBank MassBank-record Parser
parseMbRecord MassBank-record Parser
peaksMatched Select matching/unmatching peaks from aggregate table
peaksMatched-method Select matching/unmatching peaks from aggregate table
peaksUnmatched Select matching/unmatching peaks from aggregate table
peaksUnmatched-method Select matching/unmatching peaks from aggregate table
plotMbWorkspaces Plots mbWorkspaces
plotRecalibration Plot the recalibration graph.
plotRecalibration.direct Plot the recalibration graph.
ppm Calculate ppm values
problematicPeaks Identify intense peaks (in a list of unmatched peaks)
processProblematicPeaks Generate list of problematic peaks
progressBarHook Standard progress bar hook.

-- R --

readMbdata Flatten, or re-read, MassBank header blocks
reanalyzeFailpeak Reanalyze unmatched peaks
reanalyzeFailpeaks Reanalyze unmatched peaks
recalibrate Predefined recalibration functions.
recalibrate.addMS1data Return MS1 peaks to be used for recalibration
recalibrate.identity Predefined recalibration functions.
recalibrate.linear Predefined recalibration functions.
recalibrate.loess Predefined recalibration functions.
recalibrate.mean Predefined recalibration functions.
recalibrateSingleSpec Recalibrate MS/MS spectra
recalibrateSpectra Recalibrate MS/MS spectra
resetInfolists Load MassBank compound information lists
resetList Load compound list for RMassBank
RmbDefaultSettings RMassBank settings
RmbSettings RMassBank settings
RmbSettingsTemplate RMassBank settings

-- S --

selectPeaks Select peaks from aggregate table
selectPeaks-method Select peaks from aggregate table
selectSpectra Select a subset of spectra matching properties
selectSpectra-method Select a subset of spectra matching properties
setData Set 'RmbSpectrum2' data from data.frame
setData-method Set 'RmbSpectrum2' data from data.frame
show-method Workspace for 'mbWorkflow' data
show-method Workspace for 'msmsWorkflow' data
smiles2mass Calculate the mass from a SMILES-String
spectraCount Count MS2 spectra per compound
spectraCount-method Count MS2 spectra per compound

-- T --

to.limits.rcdk Convert formula to Rcdk limits
toMassbank Write MassBank record into character array
toRMB Conversion of XCMS-pseudospectra into RMassBank-spectra

-- U --

updateSettings Update settings to current version

-- V --

validate Validate MassBank records with a set of Unit tests

-- misc --

.buildRecord.RmbSpectraSet Compile MassBank records
.msmsWorkspace Workspace for 'msmsWorkflow' data
.parseTitleString Parse record title
.updateObject.RmbSpectrum2.formulaSource Add formulaSource column to spectrum.